The movie begins in an old Victorian home and shows three men discussing some business. A young girl appears in the doorway and the man calls her “Alice”. He asks Alice if she had the dream again, and she nods. The man, named Charles Kingsleigh excuses himself from the meeting and takes Alice to bed. He listens quietly to Alice, who is his daughter, as she tells him about her dream, which contained a white rabbit in a waistcoat, a blue caterpillar, and a dodo bird. She asks him if she’s gone completely mad, and he responds that she has. He then tells her that the most amazing people in the world usually are [mad]. Alice smiles, and then goes to bed.

The scene then changes to a carriage going through the countryside. We see inside the carriage is Alice (Wasikowska), and a woman who is obviously her mother. Alice seems distracted and her mother asks her if she’s been having the dream again. Alice responds ‘yes’, and asks her mother why she’s constantly having the same dream every night, then asks if most people have different dreams each night. Her mother answers that she does not know, and then asks why she forgot her corset. Alice explained that she doesn’t like going with everyone else. She then asks that if the norm were to wear a codfish on one’s head, would her mother do so. She says that the corset is the same as the codfish.

We move to a party being held, and Alice and her mother meet with Lord Ascot, a partner of Alice’s father, now deceased, and his wife. Lord Ascot’s wife then calls her son, Hamish, an extremely odd looking man, who takes Alice to the dance floor. Once again Alice begins speaking about “impossible things” and Hamish tells her to stop, and they wind up bumping into a couple on the dance floor. Hamish then takes her off the floor and tells her to meet him at the gazebo in ten minutes. Two girls, Faith and Fiona Chattaway, approach her and allude that they know a secret, and then through several confusing words to Alice, they finally admit to her that Hamish is going to ask her to marry her. Hamish’s mother then asks her to join her for a walk through the garden. She explains to Alice that she’s glad Hamish is asking her to marry him as she’ll wind up with beautiful grandchildren, and after all, her face will not remain young and she could wind up as Aunt Imogene. Through the conversation, Alice keeps saying she saw a white rabbit and eventually spots the rabbit holding up a watch, tapping it, then scampers off. Alice excuses herself and races after the rabbit. She runs into Aunt Imogene and asks if she saw it. Aunt Imogene says that she’s waiting for her fiancée who is a prince who will have to relinquish his throne to marry her. Alice then continues to search for the rabbit but eventually returns to the gazebo. Hamish starts to ask her to marry him, but Alice has to take a blue caterpillar off of his shoulder. Hamish then asks her to marry him and she says she needs time, and races off to find the rabbit. She eventually comes upon a large hole, and while looking in, falls down the hole.

Alice begins falling down the hall and winds up bouncing off a floating bed, a floating piano almost hits her, and eventually she falls through a checkered ceiling. The camera then shows an upside-down chandelier and we see Alice sitting up and her hair is straight up as through she is upside-down. The camera then pans out to show that Alice is on the ceiling and then flips around causing Alice to fall onto the ground. She gets up and starts trying the doors scattered around the room. She then finds a small door and when she tries to open it, she can’t but then notices a key on the table in the center of the room, and uses that on the door. Alice tries to climb through, but obviously can’t fit. She drinks a little bottle and coughs, then shrinks and tries the door again but it’s locked once more. At this point we start hearing two arguing voices from the keyhole saying that she isn’t the “right Alice”. Alice then winds up eating some cake and grows until she hits her head on the ceiling. She then finally grabs the key, shrinks herself down with the bottle again, and unlocks the door. She walks through and begins to look around. After a bit of walking she winds up running into the white rabbit, a mouse, a dodo bird, and two large small boys. The boys introduce themselves as Tweedle Dee and Tweedle Dum (Lucas). They keep asking her if she’s Alice and she says yes, but the mouse keeps saying she’s the wrong Alice. They decide to take her to Absolem who turns out to be a blue caterpillar who smokes a lot. He examines Alice and says that she isn’t the right Alice. The White Rabbit (Sheen) then shows Alice a large calendar that shows her looking at the calendar. Another image, dated the “Frabjous Day” shows Alice slaying what is known as the Jabberwock. Alice refuses saying she could never slay anything.

Absolem (Rickman) then disappears, and they all hear a large squawk. They look back and see a large creature and several soldiers in the shape of red playing cards. The soldiers and creature chase after them capturing the White Rabbit and the dodo bird. A man with a heart-shaped eyepatch picks up the calendar and sees the image of Alice slaying the Jabberwock. He then gets back on his horse. As the large creature races after them the mouse disappears into a tree stump and Alice and the Tweedles keep running. A large bird then picks up the two boys and we follow them for a short time as they’re taking through canyons with rocks until they reach a large castle. Alice then continues running from the creature and stops saying it’s a dream so it won’t hurt her. The creature, known as the Bandersnatch, winds up scratching her and the mouse Mallymkun (Windsor) attacks the Bandersntach, taking his eye out. Mallymkun disappears, and Alice is able to escape.

Inside the castle, we see a woman with a large head and red hair walk in. She is the Queen of Hearts (Bonham Carter), and starts questioning her frog butlers about who ate her tarts. Eventually she notices a frog looking nervous and asks him if he ate her tarts. He lies, saying no, but then the Queen takes off a bit of jelly from his lips and tastes it then says how tasty her tarts are. She exclaims off with his head, as he begs not to be killed. Stayne (Glover) the Knave of Hearts comes up and whispers to her that he had found the calendar and showed her the Frabjous Day and she asks what the girl, who Stayne tells her is Alice, is doing to her Jabberwock. When he says she’s slaying the Jabberwock she says Alice must be stopped. She is then seen on a horse outside talking to a dog named Bayard (Spall), telling him to find Alice’s scent and in return Bayard asked for his wife and children’s freedom. The Queen of Hearts promised, but after Bayard had left, her horse retorts that dogs are so easy to trick.

Eventually Alice runs into the Cheshire Cat, named Chessur (Fry), who tells her she needs something pure to heal her scratch, but he bandages her up, and then takes her to the Mad Hatter (Depp) and the March Hare (Whitehouse). We see that the March Hare, and Mallymkun are asleep at the table. They wake up and look over to Hatter who wakes up. Mallymkun once more states she’s not the real Alice, but Hatter walks onto and across the table and crouches down to see Alice, saying she is the real Alice and she’d recognize her anywhere. They start to have tea, before a barking is heard. Hatter has Alice take another potion to shrink her more, and puts her into a teakettle. Stayne, Bayard and the card soldiers have arrived. Bayard runs forward and under the table until he reaches where Hatter is holding the teakettle with Alice in it. He sniffs it, Hatter whispers Alice, and Bayard turns acting as though he had smelt Alice elsewhere. Stayne has the guards follow Bayard while he talks to Hatter and the others for a short time. Once he leaves, Hatter takes a piece of Alice’s former large dress and fashions it into a dress for the now smaller Alice.

Hatter, Alice, Mallymkun and Hare leave. Hatter then takes Alice to what appears to be a foggy area but is in fact a destroyed village. We see a flashback of where the White Queen whom Hatter served, and several villagers were enjoying their time before Stayne and the Jabberwock came and burned the village to the ground. The White Queen escaped, but Hatter returned and claimed his hat. Back in the present, Hatter is alerted by Bayard’s bark, and so Hatter rushes off but eventually realizing they wouldn’t escape. He had Alice grab onto the ribbon on his hat, and tossed his hat across the river. Hatter was then captured, and Alice eventually went to sleep. When Alice woke, Bayard had arrived but without the Hearts with him. Alice speaks with him and eventually persuades him to take her to the Queen of Hearts castle. When they arrive, Alice has to cross the moat full of heads until she slides through a crack in the wall.

Alice arrives in the Queen of Hearts garden, and watches as the Queen plays golf with a porcupine, with assistance by the White Rabbit, and the Dodo bird. Alice helps the porcupine and unties her, then is found by the White Rabbit. He scolds her for coming back, but gives her some cake to eat to grow but she chomps too much and winds up naked behind a tree and quite tall. The Queen of Hearts does not recognize Alice because of her new size, and asks what happened to her clothes and her name. Alice says her name is Um from Umbridge and she grew out of her clothes as she’s always done. The Queen orders for Alice to be given clothes and that the Queen likes Alice.

The scene changes to the White Queen’s castle where the White Queen (Hathaway) is seen speaking with her court. She then hears Bayard’s bark and excuses herself and runs to Bayard once her court is out of view. Bayard apologizes to her for taking Alice to the Red Queen’s castle, but the White Queen tells him it’s okay and to rest.

Back at the Red Queen’s castle, Alice and the Queen are in the throne room and the Queen asks for a pig as a foot rest saying she “loves a warm pig for her achy feet”. The Queen brings in the Tweedles, and at first one almost recognizes Alice but thankfully the other kicks him. The Queen asks them to talk because they talk so amusingly, but while they do when almost recognizing Alice, they wind up wandering off while the Queen laughs. The Queen then brings in Hatter, who at first recognizes Alice briefly but knows not to say anything. He then asks the Queen if he can design her hats. She agrees and he goes off to work. On the Queen’s balcony, her and Stayne talk and the Queen flirts with Stayne alluding to a romantic relationship between them.

As Alice wanders around to find Hatter, Stayne flirts with her, and one of the Queen’s court spots them. Alice finds Hatter and watches him lose his temper, but she calms him down and he keeps working. She then goes off to find the Vorpal Sword. Alice finds out it’s in the Bandersnatch’s cage, and upon finding Mallymkun, she takes the Bandersnatch’s eye and runs back to the cage opening it. She goes in and gives the creature his eye back and she reaches the sword case. Alice then sees that the key for the box is on the Bandersnatch’s neck. She is able to get the key, and the Bandersnatch licks her wound he caused, causing it to heal but still leaving a scar of the claw marks. She unlocks the box and takes the Vorpal Sword and runs back to Hatter. While in the courtyard of the castle trying on the different hats, when the woman who spotted Stayne tells the Queen. While there, Hatter notices that the woman’s large nose fell off to reveal a normal nose meaning that the court has large body parts to be part of the court, and were therefore lying to the Queen. Hatter laughs at the fat man as it’s clear he has a fat piece on. The Queen then summons Stayne back in her throne room and asks him, and he says that she seduced him. The Queen orders for her to be executed.

When Stayne goes after Alice, Mallymkun accidentally calls her “Alice” allowing Stayne to recognize her, and then is about to go after her when Hatter starts using his mannequins and hats to stop him. Alice winds up surrounded in the courtyard by the card soldiers and is about to be captured but the Bandersnatch arrives and whisks her off and they are joined by Bayard who guides them to the White Queen’s castle. The Red Queen then orders the execution of Hatter and Mallymkun.

When Alice arrives at the White Queen’s castle, the Queen is happy to see her. She is also happy to see she has returned the Vorpal Sword where it belongs. She then says that Alice is bigger than she had planned but they go to the kitchen, where the March Hare tosses items at them, which they both dodge. The White Queen then mixes a potion of dead things, explaining that the Red Queen chose to study living things, which was so much harsher. She asks Alice what she thought about her sister, and Alice responds horrid and having a bulbous head. The Queen then gives Alice a potion, which shrinks her back to perfect size. The White Queen then takes her to a part of the castle where Absolem is once again. They speak and Absolem says she looks a bit more like Alice but not completely. Alice then sighs and leaves.

In the Red Queen’s dungeon, we see Bayard’s family, and Hatter looking stoic. Chessur appears and taunts him, saying he’d like Hatter’s hat. Hatter said he’d like to look formal and that he wouldn’t give up his hat.

The next day is execution and Hatter is put against the “chopping block”. The executioner is about to take Hatter’s hat off but he asks to keep it on. Just as the executioner brings the axe down, Hatter disappears and it turns out to be Chessur having disguised himself. Hatter appears behind the Red Queen and returns to the courtyard saying that the citizens should fight back against the Queen which they begin to do, but are slowly taken down by the soldiers and the Jubjub bird. Hatter is able to save the Tweedles, Bayard’s family, and Mallymkun and get them out of the castle.

Back at the White Queen’s castle, they continue speaking about how close the Frabjous Day is coming. Then the White Queen appears to sense something, says that they have guests, looks in her telescope and sees Hatter and guests coming back. Alice then looks and takes the telescope off its stand to show Bayard as well. They greet Hatter and the others.

The next night, which happens quite quickly, Hatter and Alice speak about how the next day is the Frabjous Day. Alice admits she is nervous and cannot do it. They meet with the White Queen who asks who will be her champion. Mallymkun, Hatter, Chessur, and the Tweedles all volunteer, but having reclaimed the calendar, know the only one who can actually defeat the Jabberwock is Alice herself. The White Queen tells Alice only she can make the decision and Alice runs off unable to do it.

Alice encounters Absolem who’s turning into a chrysalis. They speak and eventually Alice realizes that the dream she had been having was of her first trip to Wonderland that she had forgotten was real. Alice realizes that she had been there and realizes she needs to fight for Wonderland, which actually was not called Wonderland but Underland and she had been the one to mistakenly call it Wonderland according to Absolem. Absolem then bid her farewell and said he may see her in another life. His chrysalis then finished forming around him and Alice left.

The scene changes to the White Queen, Hatter and the others all preparing for battle. The White Queen looks back at the gate in hope that Alice would arrive but turned back and just as she was about to order them forward, she sensed something again and turned back to see Alice come through the gate on the Bandersnatch, clad in the armor with Vorpal Sword and a shield in hand. They then marched off to the battle.

The scene changes to a giant chessboard with ruins around it. The White Hare trumpets in, as the two Queens walk forward. The White Hare announces that their champions would fight one another. The White Queen asked her sister to not let this happen, but the Red Queen burst out saying it was her crown as she was the eldest, and she should be the favorite. Alice marches forward and the Jabberwock breaks out of a large piece of land that looked like a giant boulder. He begins crushing trees until he reaches Alice. He talks to her saying he was ready to fight his nemesis, which Alice responded saying she didn’t remember him. The Jabberwock then stated that he was talking about the Vorpal Sword. Alice then told him that was enough talking, and chopped off his tongue. The two then begin battling until she gets batted away dropping the Vorpal Sword. Just as he’s about to attack her, Hatter came up and stabbed the Jabberwock in the tail.

The Red Queen exclaims that Hatter interfered causing a huge battle between the two sides. Hatter and Stayne began battling each other, the card soldiers of the Red Queen and chess soldiers of the White Queen battle, and Alice and the Jabberwock continue battling up the ruins to the side of the chessboard. Alice eventually slices off the Jabberwock’s head and it begins rolling down the ruins. Hatter is able to defeat Stayne and is about to kill him but seeing the head of the Jabberwock instead drops his sword. Alice returns to the board and watches as the soldiers drop their weapons and everyone turns on the Red Queen. The crown then floats off of the Red Queen, changing shape as it’s in the air, then Chessur appears as the one holding the crown and places it on the White Queen’s head. She then orders the Red Queen to leave Underland and is banished to the outskirts. Stayne then asks for forgiveness, but instead the White Queen has him handcuffed to the Red Queen. She sweetly says that at least they have each other, but then he attempts to either kill himself or the Queen (I’m not really sure as the Queen looked worried but I think he was going to kill himself), but Hatter swiftly sends a small pin at Stayne’s wrist causing him to drop the sword.

They then leave, and Hatter does a very interesting dance called the Futterwacken where his head moves around 360 degrees, his body moves 360 degrees, and so on. The White Queen then moves to the Jabberwock’s head. She takes a vial and takes some purple liquid from the teeth and gives it to Alice. Alice realizes that it will take her back and she turns around to Hatter. She asks him the answer to the riddle he’s been asking about the raven, and he said he had no idea what the answer was. He then asks her to stay and she says that would be lovely but she has to go, but won’t forget him. He says she will forget him, but she promises she won’t, She then drinks the potion.

Alice climbs out of the rabbit hole and returns to the gazebo. They are all rather shocked about how she looks. She just explains that she tripped and fell down a hole. Alice then goes to Hamish, says she can’t marry him because he’s not the man for her. She tells Aunt Imogene that her fiancée isn’t a prince and she should see someone about that. To Fiona and Faith, she tells them they remind her of two boys she once met. She tells her mother that she will be fine and not to worry. She also tells Hamish’s mother that she happens to like white rabbits, especially ones in waistcoats, as the mother had said she thought rabbits were filthy creatures earlier. She asks that her sister be happy with Lowell, and that Lowell treat her well, as she had spotted Lowell kissing another woman earlier in the film. Alice then talks to Lord Ascot about ideas she had about her father’s company. They adjourn to the study and she says they should be the first to trade with China. Lord Ascot tells her if he heard that from anyone else but her, he’d have thought it impossible. He then asks that while she won’t be his daughter-in-law, would she like to be an apprentice in the company?

The movie concludes with Alice on a boat, looking over to her mother and family and other citizens wishing her well. A blue butterfly then lands on her shoulder, to which Alice greets Absolem once more before he flies off into the screen as it fades to black.